String Tie with DESeq2

0

Entering edit mode

4.8 years ago

worarado.kan ▴ 20

When I run DESeq2 and showed error. Could you tell me what should I edit?

countData <- as.matrix(read.csv("genes.count.matrix3.csv", row.names="gene_id"))
Error in data[[rowvar]] : 
  attempt to select less than one element in get1index

this is my csv file

    Fuji_1  Fuji_2  Fuji_3  Gold_1  Gold_2  Gold_3
gene:MD00G1000100   0   0   0   0   0   0
gene:MD00G1000200   349 394 336 254 517 439
gene:MD00G1000300   0   0   0   0   4   0
gene:MD00G1000400   0   0   0   0   0   0
gene:MD00G1000500   403 553 303 360 376 560
gene:MD00G1000600   1271    1303    1276    1287    1304    1191

RNA-Seq • 754 views

ADD COMMENT • link updated 4.8 years ago by ATpoint 85k • written 4.8 years ago by worarado.kan ▴ 20

1

Entering edit mode

You have to give the first column a name in your CSV. Otherwise this is an incomplete field. Use a text editor or something to put a name into the first row of column1. By the way, there is not a comma in this file, you sure it is csv? Also there is no gene_id.

ADD REPLY • link 4.8 years ago by ATpoint 85k

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