Hi, I would like to get information on which samples are cases and which are controls. I am using the following commands : #creating GDS list annotgds = dbGetQuery(con,"select GDS from gds") #getting data for first 20 GDS gdslist <- sapply(annotgds[1:20,1],getGEO) #using column method get the info gds_col=sapply(gdslist[1:20],function(a) {Columns(a)} Below is the result for first two GDS: $GDS10    sample tissue        strain      disease.state                                     description 1  GSM582 spleen           NOD           diabetic           Value for GSM582: NOD_S1; src: Spleen 2  GSM589 spleen           NOD           diabetic           Value for GSM589: NOD_S2; src: Spleen 3  GSM583 spleen          Idd3 diabetic-resistant          Value for GSM583: Idd3_S1; src: Spleen 4  GSM590 spleen          Idd3 diabetic-resistant          Value for GSM590: Idd3_S2; src: Spleen 5  GSM584 spleen          Idd5 diabetic-resistant          Value for GSM584: Idd5_S1; src: Spleen 6  GSM591 spleen          Idd5 diabetic-resistant          Value for GSM591: Idd5_S2; src: Spleen 7  GSM585 spleen     Idd3+Idd5 diabetic-resistant        Value for GSM585: Idd3+5_S1; src: Spleen 8  GSM592 spleen     Idd3+Idd5 diabetic-resistant        Value for GSM592: Idd3+5_S2; src: Spleen 9  GSM586 spleen          Idd9 diabetic-resistant          Value for GSM586: Idd9_S1; src: Spleen 10 GSM593 spleen          Idd9 diabetic-resistant          Value for GSM593: Idd9_S2; src: Spleen 11 GSM587 spleen      B10.H2g7        nondiabetic      Value for GSM587: B10.H2g7_S1; src: Spleen 12 GSM594 spleen      B10.H2g7        nondiabetic      Value for GSM594: B10.H2g7_S2; src: Spleen 13 GSM588 spleen B10.H2g7 Idd3        nondiabetic Value for GSM588: B10.H2g7 Idd3_S1; src: Spleen 14 GSM595 spleen B10.H2g7 Idd3        nondiabetic Value for GSM595: B10.H2g7 Idd3_S2; src: Spleen 15 GSM596 thymus           NOD           diabetic           Value for GSM596: NOD_T1; src: Thymus 16 GSM603 thymus           NOD           diabetic           Value for GSM603: NOD_T2; src: Thymus 17 GSM597 thymus          Idd3 diabetic-resistant          Value for GSM597: Idd3_T1; src: Thymus 18 GSM604 thymus          Idd3 diabetic-resistant          Value for GSM604: Idd3_T2; src: Thymus 19 GSM598 thymus          Idd5 diabetic-resistant          Value for GSM598: Idd5_T1; src: Thymus 20 GSM605 thymus          Idd5 diabetic-resistant          Value for GSM605: Idd5_T2; src: Thymus 21 GSM599 thymus     Idd3+Idd5 diabetic-resistant        Value for GSM599: Idd3+5_T1; src: Thymus 22 GSM606 thymus     Idd3+Idd5 diabetic-resistant        Value for GSM606: Idd3+5_T2; src: Thymus 23 GSM600 thymus          Idd9 diabetic-resistant          Value for GSM600: Idd9_T1; src: Thymus 24 GSM607 thymus          Idd9 diabetic-resistant          Value for GSM607: Idd9_T2; src: Thymus 25 GSM601 thymus      B10.H2g7        nondiabetic      Value for GSM601: B10.H2g7_T1; src: Thymus 26 GSM608 thymus      B10.H2g7        nondiabetic      Value for GSM608: B10.H2g7_T2; src: Thymus 27 GSM602 thymus B10.H2g7 Idd3        nondiabetic Value for GSM602: B10.H2g7 Idd3_T1; src: Thymus 28 GSM609 thymus B10.H2g7 Idd3        nondiabetic Value for GSM609: B10.H2g7 Idd3_T2; src: Thymus $GDS100   sample       protocol      time 1 GSM549 not irradiated  0 minute 2 GSM542 not irradiated 20 minute 3 GSM543 not irradiated 60 minute 4 GSM547     irradiated  5 minute 5 GSM544     irradiated 10 minute 6 GSM545     irradiated 20 minute 7 GSM546     irradiated 40 minute 8 GSM548     irradiated 60 minute The columns are different in each GDS,so I am not able to get that information and combine it. ii) The other technique I used is the expression set.The commands for this are: eset_list <- sapply(gdslist[1:3],GDS2eSet,do.log2=TRUE) eset_col=sapply(eset_list[1:3],function(a) {pData(a)} $GDS10        sample tissue        strain      disease.state                                     description GSM582 GSM582 spleen           NOD           diabetic           Value for GSM582: NOD_S1; src: Spleen GSM589 GSM589 spleen           NOD           diabetic           Value for GSM589: NOD_S2; src: Spleen GSM583 GSM583 spleen          Idd3 diabetic-resistant          Value for GSM583: Idd3_S1; src: Spleen GSM590 GSM590 spleen          Idd3 diabetic-resistant          Value for GSM590: Idd3_S2; src: Spleen GSM584 GSM584 spleen          Idd5 diabetic-resistant          Value for GSM584: Idd5_S1; src: Spleen GSM591 GSM591 spleen          Idd5 diabetic-resistant          Value for GSM591: Idd5_S2; src: Spleen GSM585 GSM585 spleen     Idd3+Idd5 diabetic-resistant        Value for GSM585: Idd3+5_S1; src: Spleen GSM592 GSM592 spleen     Idd3+Idd5 diabetic-resistant        Value for GSM592: Idd3+5_S2; src: Spleen GSM586 GSM586 spleen          Idd9 diabetic-resistant          Value for GSM586: Idd9_S1; src: Spleen GSM593 GSM593 spleen          Idd9 diabetic-resistant          Value for GSM593: Idd9_S2; src: Spleen GSM587 GSM587 spleen      B10.H2g7        nondiabetic      Value for GSM587: B10.H2g7_S1; src: Spleen GSM594 GSM594 spleen      B10.H2g7        nondiabetic      Value for GSM594: B10.H2g7_S2; src: Spleen GSM588 GSM588 spleen B10.H2g7 Idd3        nondiabetic Value for GSM588: B10.H2g7 Idd3_S1; src: Spleen GSM595 GSM595 spleen B10.H2g7 Idd3        nondiabetic Value for GSM595: B10.H2g7 Idd3_S2; src: Spleen GSM596 GSM596 thymus           NOD           diabetic           Value for GSM596: NOD_T1; src: Thymus GSM603 GSM603 thymus           NOD           diabetic           Value for GSM603: NOD_T2; src: Thymus GSM597 GSM597 thymus          Idd3 diabetic-resistant          Value for GSM597: Idd3_T1; src: Thymus GSM604 GSM604 thymus          Idd3 diabetic-resistant          Value for GSM604: Idd3_T2; src: Thymus GSM598 GSM598 thymus          Idd5 diabetic-resistant          Value for GSM598: Idd5_T1; src: Thymus GSM605 GSM605 thymus          Idd5 diabetic-resistant          Value for GSM605: Idd5_T2; src: Thymus GSM599 GSM599 thymus     Idd3+Idd5 diabetic-resistant        Value for GSM599: Idd3+5_T1; src: Thymus GSM606 GSM606 thymus     Idd3+Idd5 diabetic-resistant        Value for GSM606: Idd3+5_T2; src: Thymus GSM600 GSM600 thymus          Idd9 diabetic-resistant          Value for GSM600: Idd9_T1; src: Thymus GSM607 GSM607 thymus          Idd9 diabetic-resistant          Value for GSM607: Idd9_T2; src: Thymus GSM601 GSM601 thymus      B10.H2g7        nondiabetic      Value for GSM601: B10.H2g7_T1; src: Thymus GSM608 GSM608 thymus      B10.H2g7        nondiabetic      Value for GSM608: B10.H2g7_T2; src: Thymus GSM602 GSM602 thymus B10.H2g7 Idd3        nondiabetic Value for GSM602: B10.H2g7 Idd3_T1; src: Thymus GSM609 GSM609 thymus B10.H2g7 Idd3        nondiabetic Value for GSM609: B10.H2g7 Idd3_T2; src: Thymus $GDS100        sample       protocol      time GSM549 GSM549 not irradiated  0 minute GSM542 GSM542 not irradiated 20 minute GSM543 GSM543 not irradiated 60 minute GSM547 GSM547     irradiated  5 minute GSM544 GSM544     irradiated 10 minute GSM545 GSM545     irradiated 20 minute GSM546 GSM546     irradiated 40 minute GSM548 GSM548     irradiated 60 minute here, also the results are same and I am not able to extract the information I need due to difference in column names. Can anyone help on this? From my another post, https://stat.ethz.ch/pipermail/bioconductor/2013-December/056361.html  I need Gene information as well but when I am looking over my gplllist object annotgpl = dbGetquery(con,"select distinct GPL from gds") gpllist <- sapply(annotgpl[1:438,1],getGEO,AnnotGPL=TRUE) genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene ID']})) This is the result of first 3 gene id's in first gpl object(GPL13) using the command above. "1""GPL13" "13""GPL13" "26""GPL13" However, I am getting altogether different gene ids's while doing it for all 3 gpl objects together as seen above.If I am doing it separately, then only i am getting the gene id's which are the correct ones, that I notice in gpllist object. The count of genes in each case (doing together vs separate )remain same . ii.) genes_new<- unlist(sapply(gpllist[1], function(a) {Table(a)[,'Gene ID']})) "818888" "GPL13" "821523" "GPL13" "824405" "GPL13" I will really appreciate any help in this. Thanks in advance, Rohan [[alternative HTML version deleted]]